: Major goals of periodontal research are to differentiate pathogenic from host compatible plaque microbiotas and to optimize treatments to convert the former to the latter. To this end, in the previous award period the composition of supra and subgingival plaques, the associations among species both within and between supra and subgingival plaques, and differences between plaques from healthy and diseased individuals were determined. One major finding was the frequent detection of anaerobic periodontal pathogens at low numbers in supragingival plaque of periodontally diseased and to a lesser extent health subjects. Weekly professional supragingival plaque removal for 3 months in 18 periodontitis subjects demonstrated astonishing reductions in the subgingival microbiota which were maintained for 9 months after cessation of the professional program. The composition of the microbiota at 12 months in theses subjects was similar to that found in periodontal health. In another of our studies, systemically administered metronidazole produced similar effects. Thus, in SA1 a 2 year randomized clinical trail will be performed comparing the effects of 1) SRP alone or in combination with 2) weekly professional supragingival plaque removal, 3) systemically administered metronidazole or 4) a combination of the 2 on clinical parameters and supra and subgingival plaque composition. 200 periodontitis patients will receive SRP under local anaesthesia and will be randomly assigned to the 4 treatment groups. All subjects will be evaluated clinically and for supra and subgingival plaque composition at 2 weeks, 3, 6, 12, 18 and 24 months. Supra and subgingival plaque samples will be taken separately from the mesial aspect of each tooth and evaluated individually for their content of 40 bacterial species using checkerboard DNA-DNA hybridization providing over 3.6 million bacterial counts. The results will determine if the beneficial effect of the individual therapies persist beyond one year and whether combined treatment produces even greater benefit to the patient. The microbial composition and ecologic relationships of supragingival plaque are less well understood than for subgingival plaque. Data from SA1 will be used in SA2 to define microbial communities in supragingival plaque using techniques that we employed to describe complexes in subgingival plaque. Patterns of colonization in both supra and subgingival plaque prior to and after therapy will also be evaluated. These data will provide a basis for understanding microbial community structure, ecological relationships and define desired microbiological end-point of therapy.